[quote=Cubist,Dec. 16 2011,15:30][/quote]I was wondering if anyone new why has the talk origins archive not any longer updated .

Also would it be possible to translate it into other languages? Any idea on who I should talk to?

Also I was wondering about the Bio-complexity org. I mean anyone can see that it's a fake pseudoscience journal, where the peer -reviewers are the same people as the editors. Doug Axe has writtne 3 out of the 5 articles and he's the managing director LOL. But If I mention it, people could answer well, it's just because you don't know enough, no real scientist has anything to say about this respectable institute.

Now I'm sure this is not true... do you have any links to science journals/scientists that indicate what this organisation really is...?

Marty

My take on that is that scientific enterprises are based on trust. If a people trust a journal... it has shown itself to be trustworthy... then people follow it and it has an impact to the scientific community.

Biologos, well, as far as I can tell, it has zero impact in the scientific community. It's not that people think it is disreputable... no one really cares.

--------------Ignored by those who can't provide evidence for their claims.

[quote=Cubist,Dec. 16 2011,15:30][/quote]I was wondering if anyone new why has the talk origins archive not any longer updated .

Also would it be possible to translate it into other languages? Any idea on who I should talk to?

Also I was wondering about the Bio-complexity org. I mean anyone can see that it's a fake pseudoscience journal, where the peer -reviewers are the same people as the editors. Doug Axe has writtne 3 out of the 5 articles and he's the managing director LOL. But If I mention it, people could answer well, it's just because you don't know enough, no real scientist has anything to say about this respectable institute.

Now I'm sure this is not true... do you have any links to science journals/scientists that indicate what this organisation really is...?

Marty

It is updated, just not very much at a time.

But we certainly could do with more submissions. That reminds me that I've been thinking of sending out a list of wanted essays to Evoldir to see if that stimulates some activity.

I was wondering if anyone new why has the talk origins archive not any longer updated .

Also would it be possible to translate it into other languages? Any idea on who I should talk to?

Also I was wondering about the Bio-complexity org. I mean anyone can see that it's a fake pseudoscience journal, where the peer -reviewers are the same people as the editors. Doug Axe has writtne 3 out of the 5 articles and he's the managing director LOL. But If I mention it, people could answer well, it's just because you don't know enough, no real scientist has anything to say about this respectable institute.

Now I'm sure this is not true... do you have any links to science journals/scientists that indicate what this organisation really is...?

Marty

My take on that is that scientific enterprises are based on trust. If a people trust a journal... it has shown itself to be trustworthy... then people follow it and it has an impact to the scientific community.

Biologos, well, as far as I can tell, it has zero impact in the scientific community. It's not that people think it is disreputable... no one really cares.

I was wondering if anyone new why has the talk origins archive not any longer updated .

Also would it be possible to translate it into other languages? Any idea on who I should talk to?

Also I was wondering about the Bio-complexity org. I mean anyone can see that it's a fake pseudoscience journal, where the peer -reviewers are the same people as the editors. Doug Axe has writtne 3 out of the 5 articles and he's the managing director LOL. But If I mention it, people could answer well, it's just because you don't know enough, no real scientist has anything to say about this respectable institute.

Now I'm sure this is not true... do you have any links to science journals/scientists that indicate what this organisation really is...?

Marty

My take on that is that scientific enterprises are based on trust. If a people trust a journal... it has shown itself to be trustworthy... then people follow it and it has an impact to the scientific community.

Biologos, well, as far as I can tell, it has zero impact in the scientific community. It's not that people think it is disreputable... no one really cares.

Bio-Complexity != Biologos

Bio-Complexity is disreputable and should be known to be so.

Sorry... I'll go away now... I am too exhausted to think.

--------------Ignored by those who can't provide evidence for their claims.

Okay and is there an association of scientific writers/scientists who have made a statement in that sense? Or at the very least single scientists that have taken apart the "research" done there?

This comes out as the ID crowed use this particular organisation calling it the only "true" science based organisation which no other scientist has refuted.

ThanksMarty

I'm not sure why one would expect an illegitimate operation to get respectful treatment in the technical literature. There's a variety of online essays going into why Douglas Axe's numbers are cooked, if that's what you want. But the pretense that balderdash is only rebutted if the rebuttals appear in the technical literature is a non-starter.

There's a variety of online essays going into why Douglas Axe's numbers are cooked, if that's what you want. But the pretense that balderdash is only rebutted if the rebuttals appear in the technical literature is a non-starter.

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I'm not sure why one would expect an illegitimate operation to get respectful treatment in the technical literature.

I don't but I would expect someone to at least denounce the fact that it's a illegitimate operation. As long as it's me or you that say so it's just our word against theirs. If it's an association of scientists or a respected journal that would be different.

Actually I don't expect the balderdash to be rebutted, except on terms of exercise for students and to expose where the errors lie. But I do expect it to be denounced as such by relevant organizations. A lot of times I get the argument see, no-body says there is something wrong with these "legitimate studies" so the logical conclusions are (1) they are legitimate and (2) they are so good that no one can disprove them.

Marty

--------------"Cows who know a moose when they see one will do infinitely better than a cow that pairs with a moose because they cannot see the difference either." Gary Gaulin

A lot of times I get the argument see, no-body says there is something wrong with these "legitimate studies" so the logical conclusions are (1) they are legitimate and (2) they are so good that no one can disprove them.

Or they are just completely irrelevant.

Bio-Complexity published three articles in 2010. Each of these articles has been cited twice according to Google Scholar.

Gauger was cited by a blog post and in an announcement.

Montanez article was cited by Ewert, who's second author of the Montanez article, and by Robert Sheldon, who posts occasionally at Uncommon Descent.

Axe's paper was cited by Sanford in The Journal of Creation and in an "article" at viXra.org, which "has been founded by scientists who find they are unable to submit their articles to arXiv.org because of Cornell University's policy of endorsements and moderation designed to filter out e-prints that they consider inappropriate." LOL.

If any of these articles were contributing anything worthwhile, they would've been cited outside of their little circlejerk. As it is, they aren't cited at all. That doesn't mean nobody can "disprove" them, it means there is no substance to be disproved.

--------------"Random mutations, if they are truly random, will affect, and potentially damage, any aspect of the organism, [...]Thus, a realistic [computer] simulation [of evolution] would allow the program, OS, and hardware to be affected in a random fashion." GilDodgen, Frilly shirt owner

Bio-Complexity published three articles in 2010. Each of these articles has been cited twice according to Google Scholar.

Gauger was cited by a blog post and in an announcement.

Montanez article was cited by Ewert, who's second author of the Montanez article, and by Robert Sheldon, who posts occasionally at Uncommon Descent.

Axe's paper was cited by Sanford in The Journal of Creation and in an "article" at viXra.org, which "has been founded by scientists who find they are unable to submit their articles to arXiv.org because of Cornell University's policy of endorsements and moderation designed to filter out e-prints that they consider inappropriate." LOL.

If any of these articles were contributing anything worthwhile, they would've been cited outside of their little circlejerk. As it is, they aren't cited at all. That doesn't mean nobody can "disprove" them, it means there is no substance to be disproved.

In a formal debate you would get no points for that argument. Don't get me wrong I do agree with you in every point but:

1) You have not shown that the articles are "unscientific"2) the measure of citation for items which are on the cutting edge of science might be expected to be low and is in any case really a subjective measure of the value of a study.3) If I write a theory of the spaghetty flying monster that explains string theory with the use of Zibibop power. Someone with a normal mind has got to denouce the fact that I've lost it especially since I have an organisation that supports the SFM and that I call myself a respectible scientist.4) If you're ignoring something you either don't know that it exists or if you do it just means that you:a) Can't find the time to call it rubbish (shameful)b) Can't find a reason to call it rubbish (verry worring)c) Can't find a problem with the item and just don't know what to do with it, which would not mean that it is not useful but that you can't understand it. (I believe that this is not the case with the Bio-complexity articles which are in fact junk).5) Just because google scholar / pub-med do not indicate results it does in no way demish the particular value that a study may have.

What are your thoughts on these pointsMarty

--------------"Cows who know a moose when they see one will do infinitely better than a cow that pairs with a moose because they cannot see the difference either." Gary Gaulin

As far as I know nobody has written a rebuttal to the Timecube guy's claims. That does not mean he's right...

Wow, I went to check the timecube thing I gotta lie down now...

The difference is that:1) Ray is not calling himself a respectable scientist2) Ray does not belong to a center that claims peer review of articles3) Ray has not published "in depth studies" using scientific jargon.

Marty

--------------"Cows who know a moose when they see one will do infinitely better than a cow that pairs with a moose because they cannot see the difference either." Gary Gaulin

In a formal debate you would get no points for that argument. Don't get me wrong I do agree with you in every point but:

1) You have not shown that the articles are "unscientific"

We've hashed Behe's article to death. It's not horribly unscientific (though is categories of loss, modification and gain are pretty subjective), but we've explained repeatedly how his paper doesn't show what it's proponents claim. Wesley linked to discussions of Axe's paper, showing why it's a crock. Quite a few other ID papers have been extensively debunked in various places as well. At some point, it becomes a game of junk-paper whack-a-mole.

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2) the measure of citation for items which are on the cutting edge of science might be expected to be low and is in any case really a subjective measure of the value of a study.

Not so. Every scientist wants to be on the cutting edge. If this stuff were perceived as actually cutting edge, it would get more citations, not less. True, citation rates are not an objective measure of importance, but they are a very good indication of whether other scientists consider important.

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3) If I write a theory of the spaghetty flying monster that explains string theory with the use of Zibibop power. Someone with a normal mind has got to denouce the fact that I've lost it especially since I have an organisation that supports the SFM and that I call myself a respectible scientist.

No. Nobody has any obligation to say a word about it. You're theory would be bogus either way. If enough people started believing you, and that affects others, then perhaps respectable people will start to denounce you. And that's exactly the case with ID & "scientific" creationism. Respectable scientists (like Elsberry) have taken the time to denounce this stuff as the crap that it is.

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4) If you're ignoring something you either don't know that it exists or if you do it just means that you:a) Can't find the time to call it rubbish (shameful)b) Can't find a reason to call it rubbish (verry worring)c) Can't find a problem with the item and just don't know what to do with it, which would not mean that it is not useful but that you can't understand it. (I believe that this is not the case with the Bio-complexity articles which are in fact junk).

It's not being ignored. It has been called rubbish, and the reasons that it's rubbish have been given repeatedly.

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5) Just because google scholar / pub-med do not indicate results it does in no way demish the particular value that a study may have.

True, but it's another indication that the study is not considered valuable.

I'm not quite sure what you're expecting here. Even if the NAS came out with a list saying "These journals and these papers are junk," so what? ID proponents would claim conspiracy, just like they have already. The real issue is whether these papers and claims hold up to scientific scrutiny, and they don't.

We've hashed Behe's article to death. It's not horribly unscientific (though is categories of loss, modification and gain are pretty subjective), but we've explained repeatedly how his paper doesn't show what it's proponents claim. Wesley linked to discussions of Axe's paper, showing why it's a crock. Quite a few other ID papers have been extensively debunked in various places as well. At some point, it becomes a game of junk-paper whack-a-mole.

Yes all points taken and used to the fullest but my reference in the case was to the Bio-complexity org. As an organization to promote "science".

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No. Nobody has any obligation to say a word about it. You're theory would be bogus either way. If enough people started believing you, and that affects others, then perhaps respectable people will start to denounce you. And that's exactly the case with ID & "scientific" creationism. Respectable scientists (like Elsberry) have taken the time to denounce this stuff as the crap that it is.

Yes Point taken, I agree totally with you. Do you have some links specific to the Bio-complexity org. I would need them on my front.

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It's not being ignored. It has been called rubbish, and the reasons that it's rubbish have been given repeatedly.

That's great can you send me some links specific to the Bio-complexity org. The only link I had was from panda's thumb that was posted here. Do you have other links?

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I'm not quite sure what you're expecting here. Even if the NAS came out with a list saying "These journals and these papers are junk," so what? ID proponents would claim conspiracy, just like they have already. The real issue is whether these papers and claims hold up to scientific scrutiny, and they don't.

Yes I understand, but you would have them on the defensive, they would be the ones who once again play the conspiracy card but that's their move.

Let me put it to you this way here's kind of how the debate is going on my front:

Someone has confronted me with 2 papers by D. Axe saying well see this proves that what we say is true. A respectable scientist has articles in a peer reviewed science journal which is of the highest standards as can be viewed in it's peer review standards.

Marty answers: Peer review my ass, D.Axe is the MD of the place and is also the author/co-author of the papers. That's one heck of a peer review that you got there.

Answer: Well so what, it's the science that counts right? and these papers show what they show and no one can deny that they are not science. They have passed a peer review (by definition of the term) the organization is bent on promoting real science, all the people involved are honest scientists that hold posts in universities. Which by the way goes to show that not all of science agrees with the evolution theory. (this last point is one of their wedges, ie. create impression that science is not unanimous on evolution theory)

No, I don't have any links that specifically denounce Bio-complexity org, nor do I have links that specifically deconstruct those papers by Axe. Axe's past work has already proven to be wrong (see Elsberry's link above). Behe's paper has already proven not to show what Ioseb and company claimed it showed.

At some point, it becomes a waste of time. People like Ioseb never admit any error, they just point to something new and say, "Well, can you disprove this?" After a while, it becomes tiresome dealing with people who don't discuss in good faith.

and these papers show what they show and no one can deny that they are not science.

So the question is what do those papers actually show?

What exactly are the claims that are being made on the basis of those papers?

Starting from Behe's paper I stated that Behe did in no way indicate that there was not enough time for evolution to take place all he said in the paper was that in the short term with the limitations clearly described in his paper, that loss was more common than gain. And that if they wanted to say that there had not been enough time they would have to prove it with some peer reviewed work.

That's when Doug Axe was ushered in with the following two claims in answer to my request:

1) The first study uses a model structured on bacteria that demonstrate the impossibility of sufficient mutational changes can take place in the time limit imposed by the age of the earth.

They quote from the article:In the end, the conclusion that complex adaptations cannot be very complex without running into feasibility problems appears to be robust. Finally, this raises the question of whether these limits to complex adaptation present a challenge to the Darwinian explanation of protein origins. The problem of explaining completely new protein structures—new folds—is so acute that it can be framedwith a very simple mathematical analysis [1]. Greater mathematical precision is needed when we consider the small-scale problem of functional diversification among proteins sharing a common fold. All such proteins are thought to have diverged through speciation and/or gene duplication events. In many cases, however, attempts to demonstrate the corresponding functional transitions in the laboratory require more than six base changes to achieveeven weak conversions (see, for example, references 28–30). Although studies of this kind tend to be interpreted as supporting the Darwinian paradigm, the present study indicates otherwise, underscoring the importance of combining careful measurements with the appropriate population models.

2) The second study analyses the changes necessary to convert two homologous enzymes which were specifically chosen to facilitate this operation.

They quote:We agree with their rejection of chance, but we argue herethat the Darwinian explanation also appears to be inadequate.Its deficiencies become evident when the focus moves fromsimilarities to dissimilarities, and in particular to functionallyimportant dissimilarities—to innovations. The extent to whichDarwinian evolution can explain enzymatic innovation seems,on careful inspection, to be very limited. Large-scale innovationsthat result in new protein folds appear to be well outsideits range [5]. This paper argues that at least some small-scaleinnovations may also be beyond its reach.

Their final comment was: "as you can see it's case closed for evolution".

Marty

--------------"Cows who know a moose when they see one will do infinitely better than a cow that pairs with a moose because they cannot see the difference either." Gary Gaulin

Specifically, I note what I think any evolutionary biologist would immediately see: that Axe and Gauger did not test an evolutionary hypothesis. Todd explains this very well, but here's the basic problem. To test an evolutionary hypothesis, as I mentioned above, one must study an evolutionary transition. In other words, one must study a change or transition from an ancestral state to a current (or later) state. Joe Thornton's work is a great example: his group examined protein function in a reconstruction of an evolutionary transition. What Axe and Gauger did was study a "transition" that has never been proposed to have happened. They examined a transition from one currently-existing protein to another currently-existing protein. It's as though they analyzed the "transition" from a cat to a dog, when they should have analyzed the transition from ancestral mammals to dogs and/or cats. Their conclusions tell us something about protein structure and function but, crucially, not about the evolution of those proteins.

This does not mean that Axe and Gauger are incorrect in their hypothesis, namely that different proteins are separated by vast evolutionary wastelands that can only be traversed with the help of "design." That may be the case. But the newly-published work in BIO-Complexity gets them no closer to establishing that hypothesis as reasonable or even likely.

No, I don't have any links that specifically denounce Bio-complexity org, nor do I have links that specifically deconstruct those papers by Axe. Axe's past work has already proven to be wrong (see Elsberry's link above). Behe's paper has already proven not to show what Ioseb and company claimed it showed.

At some point, it becomes a waste of time. People like Ioseb never admit any error, they just point to something new and say, "Well, can you disprove this?" After a while, it becomes tiresome dealing with people who don't discuss in good faith.

While I agree with you that it is time consuming and can become very tiresome (not to mention frustrating) and I'm certainly not out there to convince some people who have total blind faith and cannot reason beyond a very narrow view of the bible, I do believe that it needs to be done.

I have made some people over there reason, I have made people ask critical questions to which there was no answer beyond some vague statement like "it's the way that it is 'caus god made it that way" which is no answer at all, that's my little triumph.

I'm learning and that's always good, and many thanks to you guys.

But as the banner says above "Bring them on..." they are to chicken to do that themselves so I bring it to them.

Marty

--------------"Cows who know a moose when they see one will do infinitely better than a cow that pairs with a moose because they cannot see the difference either." Gary Gaulin

There are several HLA genes. The 673 comes from HLA-A only. There's also HLA-B and HLA-C and some other related genes.

I was trying to keep it simple, one gene with multiple alleles.

And you are totally right, except for the tactic JoeG is taking. And this why do we assume that everything has to have a scientific explanation? Why not just say that the designer could do it that way and leave it be?

I'll let you answer that one. ;)

--------------Ignored by those who can't provide evidence for their claims.

There are several HLA genes. The 673 comes from HLA-A only. There's also HLA-B and HLA-C and some other related genes.

I was trying to keep it simple, one gene with multiple alleles.

And you are totally right, except for the tactic JoeG is taking. And this why do we assume that everything has to have a scientific explanation? Why not just say that the designer could do it that way and leave it be?

I'll let you answer that one. ;)

hmm yes I get your point... why bother to think let's just let the designer™ do that for us.

Lol

--------------"Cows who know a moose when they see one will do infinitely better than a cow that pairs with a moose because they cannot see the difference either." Gary Gaulin

Meyer’s main argument for the inability of randommutation coupled with natural selection (hereafter,“RM + NS”) to add information to DNA is based onthe research of Douglas Axe, a scientist currentlyworking at the Discovery Institute’s Biologic Institute.10Meyer claims that Axe’s work demonstratesthat proteins are rare in sequence space—and arguestherefore that functional proteins cannot be convertedto different functions through RM + NS due to theintervening nonfunctional space between islands offunction. There are several reasons why Axe’s workcannot be used as evidence for such an assertion.

Meyer’s main argument for the inability of randommutation coupled with natural selection (hereafter,“RM + NS”) to add information to DNA is based onthe research of Douglas Axe, a scientist currentlyworking at the Discovery Institute’s Biologic Institute.10Meyer claims that Axe’s work demonstratesthat proteins are rare in sequence space—and arguestherefore that functional proteins cannot be convertedto different functions through RM + NS due to theintervening nonfunctional space between islands offunction. There are several reasons why Axe’s workcannot be used as evidence for such an assertion.

A mutation is a heritable change in the DNA base sequence. Epigenetics cannot, by definition, involve a change in the DNA sequence. Instead, it involves things like base modification (e.g. methylation) or alteration of the pattern of histones binding to DNA. So it's non-sensical to ask if the origin of the CIT+ mutation could be epigenetics. Just so you understand the terminology.

What you're really trying to ask is whether the CIT+ phenotype (i.e. the observed ability to use citrate as an energy source) is due to a mutation or due to some epigenetic change. I don't know the answer for a fact, but I can almost guarantee that it's due to mutation. E. coli does utilize things like methylation and histone-like proteins, but I'm not aware of any case in E. coli where an epigenetic change could cause the appearance of something like the CIT+ phenotype.

Note that I didn't bother to see if Lenski has identified a mutation responsible for the CIT+ phenotype. I'd guess that he has, but I'll let you hunt that down yourself.

"As far as science is concerned, I consider it valid only and esclusively if it is not in contrast with the word of Jehova".

ioseb might find the following observations worth think on for a while;

"In discussing questions of this kind two rules are to be observed, as Augustine teaches. The first is, to hold to the truth of Scripture without wavering. The second is that since Holy Scripture can be explained in a multiplicity of senses, one should adhere to a particular explanation only in such measure as to be ready to abandon it if it be proved with certainty to be false, lest Holy Scripture be exposed to the ridicule of unbelievers, and obstacles be placed to their believing." - Thomas Aquinas, c.a. 1225 - 1274, Summa Theologica, Prima Pars, Q68. Art 1. (1273).

“Tis a dangerous thing to engage the authority of scripture in disputes about the natural world in opposition to reason; lest time, which brings all things to light, should discover that to be evidently false which we had made scripture assert.” Telluris theoria sacra (1684 English edition, “The Sacred Theory of the Earth” Preface, pg. 10), Reverend Thomas Burnett (1635?-1715)

"If sound science appears to contradict the Bible, we may be sure that it is our interpretation of the Bible that is at fault." Christian Observer, 1832, pg. 437;

--------------"Science is the horse that pulls the cart of philosophy."

"As far as science is concerned, I consider it valid only and esclusively if it is not in contrast with the word of Jehova".

ioseb might find the following observations worth think on for a while;

"In discussing questions of this kind two rules are to be observed, as Augustine teaches. The first is, to hold to the truth of Scripture without wavering. The second is that since Holy Scripture can be explained in a multiplicity of senses, one should adhere to a particular explanation only in such measure as to be ready to abandon it if it be proved with certainty to be false, lest Holy Scripture be exposed to the ridicule of unbelievers, and obstacles be placed to their believing." - Thomas Aquinas, c.a. 1225 - 1274, Summa Theologica, Prima Pars, Q68. Art 1. (1273).

“Tis a dangerous thing to engage the authority of scripture in disputes about the natural world in opposition to reason; lest time, which brings all things to light, should discover that to be evidently false which we had made scripture assert.” Telluris theoria sacra (1684 English edition, “The Sacred Theory of the Earth” Preface, pg. 10), Reverend Thomas Burnett (1635?-1715)

"If sound science appears to contradict the Bible, we may be sure that it is our interpretation of the Bible that is at fault." Christian Observer, 1832, pg. 437;

Yes I could post them to him, but I'd rather let him do the damage that he is doing by himself to his followers.

"As far as science is concerned, I consider it valid only and esclusively if it is not in contrast with the word of Jehova".

ioseb might find the following observations worth think on for a while;

"In discussing questions of this kind two rules are to be observed, as Augustine teaches. The first is, to hold to the truth of Scripture without wavering. The second is that since Holy Scripture can be explained in a multiplicity of senses, one should adhere to a particular explanation only in such measure as to be ready to abandon it if it be proved with certainty to be false, lest Holy Scripture be exposed to the ridicule of unbelievers, and obstacles be placed to their believing." - Thomas Aquinas, c.a. 1225 - 1274, Summa Theologica, Prima Pars, Q68. Art 1. (1273).

“Tis a dangerous thing to engage the authority of scripture in disputes about the natural world in opposition to reason; lest time, which brings all things to light, should discover that to be evidently false which we had made scripture assert.” Telluris theoria sacra (1684 English edition, “The Sacred Theory of the Earth” Preface, pg. 10), Reverend Thomas Burnett (1635?-1715)

"If sound science appears to contradict the Bible, we may be sure that it is our interpretation of the Bible that is at fault." Christian Observer, 1832, pg. 437;

Yes I could post them to him, but I'd rather let him do the damage that he is doing by himself to his followers.